DETAILED CORRESPONDENCE
Status of the Application
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Applicant’s amendment to the claims, filed August 20, 2026, is acknowledged. This listing of the claims replaces all prior versions and listings of the claims.
Claims 1-3, 6, 7, 22, and 23 are pending in the application.
Applicant’s remarks filed August 20, 2026 in response to the non-final rejection filed May 20, 2026 have been fully considered.
The text of those sections of Title 35 U.S. Code not included in the instant action can be found in a prior Office action.
Restriction/Election
In response to a requirement for restriction/election filed March 27, 2024, applicant elected without traverse the invention of Group I, pending claims 1-3, 6, 7, 22, and 23, the species of phenylalanine ammonia lyase (claim 2), the species of Y0001 (no longer recited in the claims), and the species of N-caffeoyltyramine (claims 6 and 7) in the reply filed May 28, 2024.
All pending claims are drawn to the elected invention of Group I. Claims 1-3, 6, 7, 22, and 23 are being examined on the merits with claims 2, 6, and 7 being examined to the extent the claims read on the elected subject matter.
Claim Objections
The objection to claim 1 is withdrawn in view of applicant’s amendment to claim 1 to delete the conjunction “and” between parts (e) and (f) and add “and” between parts (f) and (g).
Claim Rejections - 35 USC § 112(b)
The rejection of claims 1-3, 6, 7, 22 and 23 under 35 U.S.C. 112(b) is withdrawn in view of applicant’s amendment to claim 1 to delete the phrase “that selectively ligates CoA to one or more of cinnamate, p-coumaric acid, caffeic acid, ferulic acid, or sinapic acid.”
Claim Rejections - 35 USC § 112(a)
The rejection of claims 1-3, 6, 7, 22 and 23 under 35 U.S.C. 112(a) is withdrawn in view of applicant’s amendment to claim 1 to delete the phrase “that selectively ligates CoA to one or more of cinnamate, p-coumaric acid, caffeic acid, ferulic acid, or sinapic acid.”
Claim Rejections - 35 USC § 103
Claims 1, 2, 6, 7, 22, and 23 are rejected under 35 U.S.C. 103 as being unpatentable over Hagel, J. (“Metabolic Engineering of Hydroxycinnamic Acid Amide in Nicotiana tabacum”, Dissertation, University of Calgary, 2004; cited on Form PTO-892 mailed on June 12, 2024; hereafter “Hagel”) in view of
Kang et al. (Biotechnol. Lett. 31:1469-1475, 2009; cited on the IDS filed on November 2, 2022; hereafter “Kang”),
Jiang, H. (“Metabolic Engineering of the Phenylpropanoid Pathway in Saccharomyces cerevisiae”, Dissertation, Purdue University, 2005; cited on Form PTO-892 mailed on June 12, 2024; hereafter “Jiang”),
Trantas et al. (Metabolic Engineer. 11:355-366, 2009; cited on Form PTO-892 filed December 17, 2025; hereafter “Trantas”) and
Koopman et al. (Microbial Cell Factories 11:155, 2012, 15 pages; cited on the IDS filed on November 2, 2022; hereafter “Koopman”), and
as evidenced by IUBMB Enzyme Nomenclature for EC 6.2.1.12 (obtained from https://iubmb.qmul.ac.uk/enzyme/EC6/2/1/12.html on January 30, 2025, 1 page; cited on Form PTO-892 mailed on February 4, 2025; hereafter “IUBMB”).
As amended, the claims are drawn to a recombinant eukaryotic host cell capable of producing a tyramine containing hydroxycinnamic acid amide, the recombinant eukaryotic host cell comprising:
one or more nucleic acid molecules encoding one or more enzymes capable of overproduction of L-tyrosine or L-phenylalanine, wherein at least one of said enzymes is a feedback-resistant 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase;
one or more nucleic acid molecules encoding one or more enzymes of a phenylpropanoid CoA pathway for making a hydroxycinnamoyl-CoA ester;
a nucleic acid molecule encoding a tyrosine decarboxylase that decarboxylates tyrosine to produce tyramine;
a nucleic acid molecule encoding a tyramine N-hydroxycinnamoyltransferase;
a nucleic acid molecule encoding a phenylalanine ammonia lyase to convert L-phenylalanine to cinnamic acid;
a nucleic acid molecule encoding a cinnamate-4-hydroxylase to convert cinnamic acid to coumaric acid a nucleic acid molecule encoding a cytochrome P450 reductase, wherein said cinnamate-4-hydroxylase and the cytochrome P450 reductase are coexpressed; and
a nucleic acid molecule encoding a coumaroyl CoA ligase capable of ligating CoA to one or more of cinnamate, p-coumaric acid, caffeic acid, ferulic acid, and sinapic acid into the corresponding CoA thiol esters;
wherein the recombinant eukaryotic host cell is a recombinant yeast strain, and
wherein the recombinant eukaryotic host cell comprises a knockout of ARO10 and a knockout of PDC5.
The following explanation is provided for clarity of the record. The rejection refers to the enzyme abbreviations DAHP synthase, PAL, C4H, CPR, 4CL, TYDC, and THT.
DAHP is the abbreviation for 3-deoxy-D-arabino-heptulosonate-7-phosphate and DAHP synthase corresponds to “one or more enzymes capable of overproduction of L-tyrosine” in part (a) of claim 1.
TYDC is the abbreviation for tyrosine decarboxylase and corresponds to a tyrosine decarboxylase that decarboxylates tyrosine to produce tyramine in part (c) of claim 1.
THT is the abbreviation for tyramine N-hydroxycinnamoyltransferase and corresponds to part (d) of claim 1.
PAL is the abbreviation for phenylalanine ammonia lyase and corresponds to “one or more enzymes of a phenylpropanoid CoA pathway for making a hydroxycinnamoyl-CoA ester” in part (b) of claim 1, “a phenylalanine ammonia lyase to convert L-phenylalanine to cinnamic acid” in part (e) of claim 1, and “phenylalanine ammonia lyase” in claim 2.
C4H is the abbreviation for cinnamate-4-hydrolyase and corresponds to “one or more enzymes of a phenylpropanoid CoA pathway for making a hydroxycinnamoyl-CoA ester” in part (b) of claim 1 and “a cinnamate-4-hydroxylase to convert cinnamic acid to coumaric acid” in part (f) of claim 1.
CPR is the abbreviation for cytochrome P450 reductase and corresponds to “one or more enzymes of a phenylpropanoid CoA pathway for making a hydroxycinnamoyl-CoA ester” in part (b) of claim 1 and “cytochrome P450 reductase” in part (f) of claim 1.
4CL is the abbreviation for 4-coumarate:CoA ligase or as evidenced by IUBMB, is alternatively referred to as p-coumaroyl CoA ligase (see “Accepted name” and “Other name(s)”). 4CL corresponds to “one or more enzymes of a phenylpropanoid CoA pathway for making a hydroxycinnamoyl-CoA ester” in part (b) of claim 1 and “a coumaroyl CoA ligase capable of ligating CoA to one or more of cinnamate, p-coumaric acid, caffeic acid, ferulic acid, and sinapic acid into the corresponding CoA thiol esters” in part (g) of claim 1.
Figure 3 of Hagel (reproduced in Appendix A for convenience and clarity of the record) shows a simplified scheme for the biosynthesis of the hydroxycinnamic acid amides, 4-coumaroyltyramine and feruloyltyramine, in plants (pp. 10-11). Hagel teaches important enzymes in the biosynthesis of hydroxycinnamic acid amides in plants including PAL, 4CL, TYDC, and THT (p. 14, bottom to p. 24, middle). Hagel teaches 4CL catalyzes the last step of the general phenylpropanoid pathway and converts 4-coumaric acid to the corresponding CoA ester (p. 15, first full paragraph). Figure 7 of Hagel (reproduced in Appendix A for convenience and clarity of the record) depicts the phenylpropanoid pathway showing biosynthesis of hydroxycinnamic acid amides, which includes C4H to convert cinnamate to 4-coumarate (pp. 31-32). Hagel teaches a transgenic tobacco plant designated as “TYDC x THT,” which is engineered to overexpress TYDC and THT for the increased production of tyramine-derived hydroxycinnamic acid amide (p. iii, Abstract; p. 49, second paragraph).
Hagel teaches engineering a tobacco plant for production of tyramine-derived hydroxycinnamic acid amide but does not teach a recombinant yeast strain for production of hydroxycinnamic acid amides.
Kang teaches tyramine derivatives are synthesized in trace amounts in plants and that in contrast to using plants as hosts for producing plant specific secondary metabolites, the use of microbes provides a good alternative for the mass production of scarce bioactive compounds (p. 1469, column 1, bottom to p. 1470, column 2, top). Kang teaches an E. coli modified to express 4CL and THT, which, when combined with tyramine, produced large amounts of feruloyltyramine, 4-coumaroyltyramine, and caffeoyltyramine (p. 1470, sentence bridging columns 1-2).
Jiang teaches that S. cerevisiae has some advantages over E. coli for expressing eukaryotic heterologous proteins (p. 14, bottom) and Trantas teaches S. cerevisiae as a eukaryotic organism has transcriptional and translational mechanisms similar in basic respects to those of plants, making yeast a suitable single-celled organism for the production of secondary metabolites through the heterologous expression of plant genes (p. 361, column 2, bottom). Jiang teaches the phenylpropanoid pathway in plants (p. 10, Figure 1.2, reproduced in Appendix B for convenience and clarity of the record) including PAL, C4H, and 4CL (p. 16, middle) and suggests transferring a plant phenylpropanoid pathway into yeast for the production of desired downstream products (p. 16, middle). Similar to Jiang, Trantas discusses the phenylpropanoid pathway in plants including PAL, C4H, and 4CL (p. 356, column 1, middle), however, Trantas teaches the additional expression of CPR with the phenylpropanoid pathway enzymes enhanced p-coumaric acid production by 4-fold and teaches the phenylpropanoid pathway in yeast requires the support of a plant CPR (p. 359, column 2). Trantas teaches a metabolically engineered S. cerevisiae strain expressing PAL, C4H, 4CL, and CPR for production of downstream products from the intermediate 4-coumaroyl-CoA (p. 360, Figure 2, reproduced in Appendix C for convenience and clarity of the record).
In view of the combined teachings of Hagel, Kang, Jiang, and Trantas, it would have been obvious to one of ordinary skill in the art before the effective filing date for a S. cerevisiae expressing PAL, C4H, 4CL, CPR, TYDC, and THT in order to produce hydroxycinnamic acid amides.
One would have been motivated to do so because while Hagel teaches recombinantly expressing TYDC and THT in a plant in order to convert 4-coumaroyl-CoA of the phenylpropanoid pathway and tyramine to hydroxycinnamic acid amides, Kang teaches that tyramine derivatives are synthesized in only trace amounts in plants. As an alternative, Kang teaches using microbes for the mass production of scarce bioactive compounds, and while Kang selected E. coli as the microbe for production of hydroxycinnamic acid amides, Jiang acknowledges that S. cerevisiae has advantages over E. coli for expression of eukaryotic genes and Trantas teaches S. cerevisiae as a eukaryotic organism has transcriptional and translational mechanisms similar in basic respects to those of plants making yeast a suitable single-celled organism for the production of secondary metabolites through the heterologous expression of plant genes. Trantas teaches metabolically engineering S. cerevisiae with the plant phenylpropanoid pathway enzymes PAL, C4H, 4CL, and CPR to produce the 4-coumaroyl-CoA intermediate as a metabolite for biosynthesis of plant-based compounds.
One would have expected success because the TYDC and THT taught by Hagel and Kang are eukaryotic enzymes and Jiang taught S. cerevisiae as a suitable host for the expression of eukaryotic polypeptides and Trantas taught S. cerevisiae as a eukaryotic organism has transcriptional and translational mechanisms similar in basic respects to those of plants making yeast a suitable single-celled organism for the production of secondary metabolites through the heterologous expression of plant genes.
Regarding the limitations “(a) one or more nucleic acid molecules encoding one or more enzymes capable of overproduction of L-tyrosine or L-phenylalanine, wherein at least one of said enzymes is a feedback-resistant 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase” and “wherein the recombinant eukaryotic host cell comprises a knockout of ARO10 and a knockout of PDC5” in claim 1, as shown by Hagel, tyrosine and phenylalanine are substrates for hydroxycinnamic acid amide production (p. 10 and Figure 3) and Jiang teaches that L-Tyr pool size is limiting in S. cerevisiae overexpressing PAL (p. 59) and the S. cerevisiae could be engineered to increase flux to L-Phe and L-Tyr (p. 98, bottom). Jiang teaches a DAHP synthase mutant free from feedback inhibition and expressing the mutant DAHP synthase increased L-Tyr production (p. 99). Koopman teaches expressing a mutant DAHP synthase in S. cerevisiae and knocking out ARO10 and PDC5 to enhance the availability of the aromatic amino acids L-Phe and L-Tyr (p. 5, columns 1-2).
In view of the teachings of Jiang and Koopman, it would have been obvious to one of ordinary skill in the art before the effective filing date to further modify a S. cerevisiae expressing PAL, C4H, 4CL, CPR, TYDC, and THT as taught and/or suggested by the combination of Hagel, Kang, Jiang, and Trantas to express a feedback-resistant DAHP synthase and to knockout ARO10 and PDC5.
One would have been motivated and would have expected success because Hagel taught tyrosine and phenylalanine are substrates for hydroxycinnamic acid amide production, Jiang taught the S. cerevisiae could be engineered to increase flux to L-Phe and L-Tyr, which are aromatic amino acids, Jiang and Koopman taught expressing a feedback-resistant DAHP synthase to increase aromatic amino acid production, and Koopman taught knocking out ARO10 and PDC5 to reduce the diversion of aromatic amino acid biosynthesis.
Therefore, claims 1, 2, 6, 7, 22, and 23 would have been obvious to one of ordinary skill in the art before the effective filing date.
Claim 3 is rejected under 35 U.S.C. 103 as being unpatentable over Hagel in view of Kang, Jiang, Trantas, and Koopman and as evidenced by IUBMB as applied to claims 1, 2, 6, 7, 22, and 23 above, and further in view of Cao et al. (Ann. Microbiol. 62:1395-1402, 2012; cited on the attached Form PTO-892; hereafter “Cao”).
Claim 3 is drawn to the recombinant eukaryotic host cell of claim 1, wherein said host cell further overproduces S-adenosylmethionine.
The relevant teachings of Hagel, Kang, Jiang, Trantas, and Koopman and evidentiary reference IUBMB as applied to claims 1, 2, 6, 7, 22, and 23 are set forth above.
The combination of Hagel, Kang, Jiang, Trantas, and Koopman does not teach or suggest overproducing S-adenosylmethionine.
Cao teaches S-adenosyl-L-methionine (SAM) is an essential metabolite in all living cells, plays an important role in cellular functions (p. 1395, column 1, Abstract), and exhibits pivotal roles in various biological reactions (p. 1395, column 2, top). Cao teaches subjecting a S. cerevisiae to mutagenesis with UV irradiation to achieve a rapid improvement of SAM production (p. 1395, column 1, Abstract) and teaches various other alternative methods of enhancing SAM production by S. cerevisiae (p. 1399, column 2 and p. 1400, column 2).
In view of the combined teachings of Hagel, Kang, Jiang, Trantas, Koopman, and Cao, it would have been obvious to one of ordinary skill in the art before the effective filing date for the S. cerevisiae expressing PAL, C4H, 4CL, CPR, TYDC, and THT as taught and/or suggested by the combination of Hagel, Kang, Jiang, and Trantas to overproduce SAM. One would have been motivated in order to optimize the S. cerevisiae expressing PAL, C4H, 4CL, CPR, TYDC, and THT as taught and/or suggested by the combination of Hagel, Kang, Jiang, and Trantas because Cao taught SAM is an essential metabolite in all living cells, plays an important role in cellular functions, and exhibits pivotal roles in various biological reactions. One would have expected success because Cao taught multiple methods of enhancing SAM production by S. cerevisiae.
Therefore, claim 3 would have been obvious to one of ordinary skill in the art before the effective filing date.
RESPONSE TO REMARKS: At p. 7 of the instant remarks, applicant argues the reason given for combining the references is that 4-coumaroyl-CoA made by the yeast of Trantas is the same intermediate that is combined with tyramine to produce hydroxycinnamic acid amides as taught by Hagel and Kang.
Applicant’s argument is not found persuasive. Contrary to applicant’s position, the applicant’s cited statement at p. 16 of the previous Office action was (and is) not included in the rejections under 35 U.S.C. 103. Moreover, the reasons for combining the cited prior art do not solely rely on the teachings of Trantas as implied by applicant’s argument. Rather, the obviousness rationale is based on a combination of teachings of Hagel, Kang, Jiang, Trantas, and Koopman.
At p. 8 of the instant remarks, applicant argues claim 1 is not a list of enzymes but is a eukaryotic cell in which each of the following is required to occur: aromatic amino acid supply is engineered, by a feedback-resistant DAHP synthase together with knockouts of ARO10 and PDC5, so that the cell overproduces L-tyrosine or L-phenylalanine; those amino acids are converted within the cell to a hydroxycinnamoyl-CoA pool by PAL, by a cinnamate-4-hydroxylase coexpressed with a cytochrome P450 reductase, and by a coumaroyl CoA ligase; tyramine is generated within the same cell by a tyrosine decarboxylase acting on the tyrosine the cell itself has made; and the two internally generated pools are joined by a tyramine N-hydroxycinnamoyltransferase to give the tyramine-containing hydroxycinnamic acid amide. Applicant argues the subject matter of claim 1 is the coupling of the engineered production of the substrates and the production of the tyramine-containing hydroxycinnamic acid amide from these substrates and it is the coupled architecture – not a listing of enzymes – that the cited prior art must show to have been obvious.
Applicant’s arguments are not found persuasive. Applicant’s description of claim 1 does not reflect claim 1 as filed on August 20, 2026. Although the claims are interpreted in light of the specification, limitations from the specification are not read into the claims. See MPEP 2145.VI. For the reasons set forth in the rejections under 35 U.S.C. 103, the combination of Hagel, Kang, Jiang, Trantas, and Koopman teach all claim limitations and provide motivation and a reasonable expectation of success to make the claimed recombinant eukaryotic host cell.
Beginning at p. 8 of the instant remarks, applicant cites to the references of Kang, Hagel, and Trantas and argues that Kang discloses an E. coli expressing 4CL and THT but the substrates are supplied for amide formation, Hagel discloses a tobacco plant overexpressing TYDC and THT with amide formation but the plant already possesses both substrate pools, and Trantas discloses a yeast cell producing 4-coumaroyl-CoA but not the amine acceptor or transferase. Applicant contends that the combination of cited references does not teach or suggest the claimed recombinant eukaryotic host cell, particularly a tyramine N-hydroxycinnamoyltransferase acting on substrate pools generated within the cell by an engineered pathway.
Applicant’s arguments are not found persuasive. The rejection is based on a combination of cited teachings of Hagel, Kang, Jiang, Trantas, and Koopman and for reasons described in detail above, a S. cerevisiae expressing PAL, C4H, 4CL, CPR, TYDC, THT, and a feedback-resistant DAHP synthase and with knockout of ARO10 and PDC5 for the production of tyramine-containing hydroxycinnamic acid amides would have been obvious to one of ordinary skill in the art before the effective filing date.
At p. 9 of the instant remarks, Applicant reiterates the position that the rejection’s reason for combining the references is that 4-coumaroyl-CoA of Trantas is the same intermediate that Hagel and Kang condense with tyramine. Applicant argues that while the identity of the 4-coumaroyl-CoA establishes the proposed modification is possible, it does not supply a reason why one of ordinary skill would have made such a modification.
Applicant’s argument is not found persuasive. Contrary to applicant’s position, the applicant’s cited statement at p. 16 of the previous Office action was (and is) not included in the rejections under 35 U.S.C. 103. Moreover, the reasons for combining the cited prior art do not solely rely on the teachings of Trantas as implied by applicant’s argument. Rather, the obviousness rationale is based on the combination of Hagel, Kang, Jiang, Trantas, and Koopman and for reasons described in detail above, the claimed recombinant eukaryotic host cell would have been obvious to one of ordinary skill in the art before the effective filing date.
Beginning at p. 9 of the instant remarks, applicant cites to Jiang’s Figure 1.2 and Trantas’ Figure 2, which show 4-coumaroyl-CoA as an intermediate of numerous downstream products. Applicant contends that based on the Office’s reasoning, any downstream product of 4-coumaroyl-CoA would have been obvious with the yeast of Trantas, however, this reasoning is not sufficient to establish obviousness.
Applicant’s arguments are not found persuasive. The examiner acknowledges that 4-coumaroyl-CoA is an intermediate of numerous downstream products. However, contrary to applicant’s position, the obviousness rationales presented in the rejections under 35 U.S.C. 103 are not directed to any downstream product of 4-coumaroyl-CoA but rather specifically address the claimed invention.
At p. 10 of the remarks, applicant argues that while the rejection identifies features of the claimed invention in the cited prior art, it is only the applicant’s specification that assembles them according to claim 1, however, claim 1 may not serve as the template against which the prior art is gathered.
In response to applicant's argument that the examiner's conclusion of obviousness is based upon improper hindsight reasoning, it must be recognized that any judgment on obviousness is in a sense necessarily a reconstruction based upon hindsight reasoning. But so long as it takes into account only knowledge which was within the level of ordinary skill at the time the claimed invention was made and does not include knowledge gleaned only from the applicant's disclosure, such a reconstruction is proper. See MPEP 2145.X.A. In this case, the obviousness rationales take into account only knowledge that was within the level of ordinary skill at the time the claimed invention was made and does not include knowledge gleaned only from the applicant's disclosure.
At p. 10 of the remarks, applicant argues Jiang and Trantas do not provide a reasonable expectation that a yeast comprising a heterologous THT will capture a heterologously generated hydroxycinnamoyl-CoA pool in the presence of that host's own acyl CoA metabolism, using tyramine that the same engineered cell must simultaneously generate from its own tyrosine. Applicant argues that the Office has made no finding as to the operation of THT on internally generated substrate pools in any yeast.
Applicant’s argument is not found persuasive. In this case, it appears applicant is requiring absolute predictability of success in order to establish obviousness of the claimed invention. However, according to MPEP 2143.02.II, obviousness does not require absolute predictability of success, only some degree of predictability is required. In view of the combined teachings of the cited prior art, one of ordinary skill would have had at least some degree of predictability for a S. cerevisiae expressing PAL, C4H, 4CL, CPR, TYDC, THT, and a feedback-resistant DAHP synthase and with knockout of ARO10 and PDC5 and that such a S. cerevisiae would be capable of producing tyramine-containing hydroxycinnamic acid amides.
For these reasons, it is the examiner’s position that the claimed invention would have been prima facie obvious to one of ordinary skill in the art before the effective filing date.
Conclusion
Status of the claims:
Claims 1-3, 6, 7, 22, and 23 are pending in the application.
Claims 1-3, 6, 7, 22, and 23 are rejected.
No claim is in condition for allowance.
THIS ACTION IS MADE FINAL. Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to DAVID J STEADMAN whose telephone number is (571)272-0942. The examiner can normally be reached Monday to Friday, 7:30 AM to 4:00 PM.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, MANJUNATH N. RAO can be reached on 571-272-0939. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/David Steadman/Primary Examiner, Art Unit 1656
APPENDIX A
Figures 3 (top) and 7 (bottom) of Hagel
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712
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APPENDIX B
Figure 1.2 of Jiang
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APPENDIX C
Figure 2 of Trantas
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Prosecution Insights